Pin numpy to <2.0 to fix zarr compatibility #48
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Specify docker image for dev environments
Update dockerfile for dev envs
Update dockerfile
…tch-1 Add badges to readme
Update ome_types version
Add logo to README.md
…fig, fix allOf references Co-authored-by: adamjtaylor <14945787+adamjtaylor@users.noreply.github.com>
Co-authored-by: adamjtaylor <14945787+adamjtaylor@users.noreply.github.com>
Co-authored-by: adamjtaylor <14945787+adamjtaylor@users.noreply.github.com>
Co-authored-by: adamjtaylor <14945787+adamjtaylor@users.noreply.github.com>
…tch-1 Fix samplesheet location for test profile
Co-authored-by: adamjtaylor <14945787+adamjtaylor@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: adamjtaylor <14945787+adamjtaylor@users.noreply.github.com>
…tional-save-for-images Feature merge into branch to unblock rapidly
Co-authored-by: adamjtaylor <14945787+adamjtaylor@users.noreply.github.com>
…oken-schema-references Fix broken schema references preventing Seqera Platform launch
…tional-save-for-images Add optional publishDir for bioformats2ometiff converted images
…d-failing Fix dockerfile
The zarr library uses np.PINF which was removed in NumPy 2.0. This constraint prevents pip installs from upgrading numpy beyond 1.x. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Closing - PR was created on wrong repo. See Sage-Bionetworks-Workflows#41 |
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Summary
>=1.23.0,<2.0in Docker environmentProblem
The zarr library uses
np.PINFwhich was removed in NumPy 2.0. Pip installs in the Dockerfile can upgrade numpy beyond the conda-pinned version, causing this error:This blocks all CI tests including PR #37 (H&E RGB thumbnail generation).
Fix
Changed from exact pin
numpy=1.23.0to rangenumpy>=1.23.0,<2.0to prevent any numpy 2.x installation while allowing patch updates.Testing
Once merged, Docker container will rebuild automatically. This unblocks testing for PR #37.
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